Origin IGS: aagccgtcctaaccgaatatctttttcatcttatactaaaactatataagatacaataggtcaaattaatgtttttagatactcagaataggacggctactgaatcgttatt .........1.........2.........3.........4.........5.........6.........7.........8.........9.........1.........2.........3.........4.........5.........6.........7.........8.........9 aataacgattcagtagccgtcctattctgagtatctaaaaacattaatttgacctattgtatcttatatagttttagtataagatgaaaaagatattcggttaggacggctt Mask Tandem Repeat Region ================================================ aagccgtcctaaccgaatatctttttcatcttatactaaaactatataagatacaataggtcaaattaatgtttttagatactcagaataggacggctactgaatcgttatt Find is-nt database================================================ Query_seq: TDE0801:TDE0802|TDE0801:TDE0802:hypothetical protein:hypothetical protein:<-<-:824450..824561 112 aagccgtcctaaccgaatatctttttcatcttatactaaaactatataagatacaataggtcaaattaatgtttttagatactcagaataggacggctactgaatcgttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find is-aa database================================================ Query_seq: TDE0801:TDE0802|TDE0801:TDE0802:hypothetical protein:hypothetical protein:<-<-:824450..824561 112 aagccgtcctaaccgaatatctttttcatcttatactaaaactatataagatacaataggtcaaattaatgtttttagatactcagaataggacggctactgaatcgttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 Find nr database================================================ Query_seq: TDE0801:TDE0802|TDE0801:TDE0802:hypothetical protein:hypothetical protein:<-<-:824450..824561 112 aagccgtcctaaccgaatatctttttcatcttatactaaaactatataagatacaataggtcaaattaatgtttttagatactcagaataggacggctactgaatcgttatt Intra-Species Hit: Count: 0 Inter-species Hit: Count: 0 aagccgtcctaaccgaatatctttttcatcttatactaaaactatataagatacaataggtcaaattaatgtttttagatactcagaataggacggctactgaatcgttatt Predict ORF larger than 30AA ================================================ aagccgtcctaaccgaatatctttttcatcttatactaaaactatataagatacaataggtcaaattaatgtttttagatactcagaataggacggctactgaatcgttatt Predict Promoter with matrix: RpoD-15 score > 80================================================ Predict Promoter with matrix: RpoD-16 score > 80================================================ Predict Promoter with matrix: RpoD-17 score > 80================================================ Predict Promoter with matrix: RpoD-18 score > 80================================================ Predict Promoter with matrix: RpoD-19 score > 80================================================ Predict Promoter with matrix: RpoN score > 80================================================ aagccgtcctaaccgaatatctttttcatcttatactaaaactatataagatacaataggtcaaattaatgtttttagatactcagaataggacggctactgaatcgttatt Predict TransTerm conf > 70================================================ Find igs database================================================ Query_seq: TDE0801:TDE0802|TDE0801:TDE0802:hypothetical protein:hypothetical protein:<-<-:824450..824561 112 aagccgtcctaaccgaatatctttttcatcttatactaaaactatataagatacaataggtcaaattaatgtttttagatactcagaataggacggctactgaatcgttatt Intra-Species Hit: Count: 1 Min: 1 Max: 112 Len: 112 Subject: NC_002967_TDE0801_TDE0802|hypothetical protein:hypothetical protein|NEGATIVE:NEGATIVE|[824450,824561]|112 HSP 1 e-value: 2.0E-57 bit: 222.0 Len: 112 Query Start:1 Query End:112 Subject Strand: POSITIVE Subject Start: 1 Subject End: 112 aagccgtcctaaccgaatatctttttcatcttatactaaaactatataagatacaataggtcaaattaatgtttttagatactcagaataggacggctactgaatcgttatt aagccgtcctaaccgaatatctttttcatcttatactaaaactatataagatacaataggtcaaattaatgtttttagatactcagaataggacggctactgaatcgttatt Inter-species Hit: Count: 0 Predict Forward Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAGCCGUCCUAACCGAAUAUCUUUUUCAUCUUAUACUAAAACUAUAUAAGAUACAAUAGGUCAAAUUAAUGUUUUUAGAUACUCAGAAUAGGACGGCUACUGAAUCGUUAUU .((((((((((..(((.(((((.....((((((((.........))))))))(((.(((......))).)))....))))).)).)..)))))))))).............. (-25.90) Predict Reverse Strand Minimun Free Energy by RNAFold (ViennaRNA) ================================================ AAUAACGAUUCAGUAGCCGUCCUAUUCUGAGUAUCUAAAAACAUUAAUUUGACCUAUUGUAUCUUAUAUAGUUUUAGUAUAAGAUGAAAAAGAUAUUCGGUUAGGACGGCUU ..............((((((((((..((((((((((.....((......))........((((((((((.......))))))))))....)))))))))).)))))))))). (-38.10) Find mRNA Target Using Conserved IGS================================================ 5'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 790 110 61 201 152 NC_002967:TDE0801|5end_hypothetical_protein_824359..824589_NEGATIVE 253 100 53 231 172 NC_002967:TDE2089|5end_signal_recognition_particle_protein_2117563..2117793_NEGATIVE 227 33 3 205 179 NC_002967:TDE1641|5end_ribose_5-phosphate_isomerase_A_1691877..1692107_POSITIVE 227 45 2 181 144 NC_002967:TDE1254|5end_Smr_domain_protein_1288411..1288641_POSITIVE 226 36 2 98 52 NC_002967:TDE1682|5end_V-type_ATP_synthase_subunit_B_1734843..1735073_NEGATIVE 217 41 2 164 121 NC_002967:TDE1649|5end_hypothetical_protein_1697437..1697667_NEGATIVE 217 20 1 135 115 NC_002967:TDE1600|5end_ABC_transporter,_ATP-binding/permease_protein_1652396..1652626_NEGATIVE 217 27 2 77 48 NC_002967:TDE0820|5end_transcriptional_regulator,_TetR_family_844373..844603_NEGATIVE 216 35 1 158 127 NC_002967:TDE0943|5end_hypothetical_protein_965983..966213_POSITIVE 213 49 2 57 4 NC_002967:TDE1185|5end_lipoprotein,_putative_1212973..1213203_NEGATIVE 213 34 1 58 24 NC_002967:TDE1050|5end_hypothetical_protein_1077387..1077617_POSITIVE 203 46 4 127 85 NC_002967:TDE2747|5end_type_I_restriction-modification_system,_R_subunit_2804942..2805172_NEGATIVE 203 33 1 95 55 NC_002967:TDE1237|5end_hypothetical_protein_1270368..1270598_POSITIVE 201 38 1 96 56 NC_002967:TDE1039|5end_riboflavin_biosynthesis_protein,_putative_1067072..1067302_POSITIVE 200 110 74 152 118 NC_002967:TDE2107|5end_dihydroorotase,_putative_2132874..2133104_NEGATIVE 200 32 4 202 167 NC_002967:TDE2004|5end_hypothetical_protein_2023622..2023852_POSITIVE 199 45 2 91 44 NC_002967:TDE2588|5end_integrase_domain_protein_2623496..2623726_POSITIVE 199 110 69 185 135 NC_002967:TDE0048|5end_hypothetical_protein_57822..58052_NEGATIVE 198 50 2 109 52 NC_002967:TDE2342|5end_1-deoxy-D-xylulose_5-phosphate_reductoisomerase_2380383..2380613_NEGATIVE 198 110 80 182 156 NC_002967:TDE0768|5end_50S_ribosomal_protein_L4_806996..807226_POSITIVE 3'END mRNA Target Prediction=================================== Score srna_start srna_end target_start tegart_end seq_id 226 36 2 96 50 NC_002967:TDE1683|3end_V-type_ATP_synthase_subunit_A_1734845..1734995_NEGATIVE 217 20 1 142 122 NC_002967:TDE1601|3end_transcriptional_regulator,_TetR_family_1652389..1652539_NEGATIVE 217 110 69 93 48 NC_002967:TDE0741|3end_hypothetical_protein_776185..776335_NEGATIVE 216 35 1 34 3 NC_002967:TDE0942|3end_long-chain-fatty-acid--CoA_ligase,_putative_965939..966089_POSITIVE 213 34 1 45 11 NC_002967:TDE1049|3end_elongation_factor_EF-2_1077454..1077604_POSITIVE 213 43 4 144 102 NC_002967:TDE0406|3end_hypothetical_protein_458929..459079_POSITIVE 200 110 74 124 90 NC_002967:TDE2108|3end_hypothetical_protein_2132902..2133052_NEGATIVE 200 43 4 128 82 NC_002967:TDE2096|3end_hypothetical_protein_2124491..2124641_POSITIVE 200 32 4 131 96 NC_002967:TDE2003|3end_internalin-related_protein_2023631..2023781_POSITIVE 198 50 2 109 52 NC_002967:TDE2343|3end_phosphatidate_cytidylyltransferase_2380383..2380533_NEGATIVE 198 32 3 57 29 NC_002967:TDE0200|3end_tetrapyrrole_methylase_family_protein_235372..235522_POSITIVE 195 17 3 150 136 NC_002967:TDE0809|3end_hypothetical_protein_829640..829790_NEGATIVE 195 48 13 42 1 NC_002967:TDE0160|3end_hypothetical_protein_187145..187295_NEGATIVE 194 43 3 50 5 NC_002967:TDE2162|3end_NOL1/NOP2/sun_family_protein_2195560..2195710_POSITIVE 192 97 52 132 86 NC_002967:TDE2063|3end_ferrous_iron_transport_protein_B_2088430..2088580_NEGATIVE 192 30 3 149 118 NC_002967:TDE1238|3end_translocase_1271245..1271395_POSITIVE 192 29 3 48 27 NC_002967:TDE1101|3end_acetyltransferase,_GNAT_family_1134663..1134813_NEGATIVE 190 98 51 72 28 NC_002967:TDE0683|3end_hypothetical_protein_721187..721337_NEGATIVE 186 43 3 141 100 NC_002967:TDE1208|3end_DNA_topoisomerase_I_1242432..1242582_POSITIVE 185 35 3 148 117 NC_002967:TDE0012|3end_carbon_starvation_protein_CstA,_putative_17702..17852_POSITIVE